When I ran this, the transforms run correctly and the content is updated, but the bundletransformer library reads the file instead of the response content and completely ignores all other transforms.

It would be nice if it can read the response content instead of the file because the response content already has the contents from all the files in the bundle. MVC already gives us this. You could avoid an unnecessary file read and make the solution more extendible.

Is it possible to maybe add a configurable option to use content instead of reading the file again?

I tried the solution and it works fine, except that it doesnt work in debug mode.

On Stack Overflow in comments described solution for this problem:

Hernan! In Bundle Transformer 1.9.0 Beta 1 implemented this functionality - bundletransformer.codeplex.com/releases/view/123398. In order to the debugging HTTP-handlers can use a transformations from bundles need to add in the
RegisterBundles method of App_Start/BundleConfig.cs file the following code:
BundleResolver.Current = new CustomBundleResolver();